However, Despite other adversaries such as Mr. X appearing as the villain, Dr. Wily still ends up being the final boss in the end.

Dr. Wily, Dr. Light's assistant, who is angry that his contributions have not been acknowledged by the world, reprograms the six Robot Masters (Bomb Man, Guts Man, Cut Man, Elec Man, Ice Man and Fire Man) that they had designed for industrial purposes and uses them in an attempt at world domination.